J. Biomedical Science and Engineering, 2017, 10, 172-181
http://www.scirp.org/journal/jbise
ISSN Online: 1937-688X
ISSN Print: 1937-6871
Comparison of Two Possible Evolutionary
Mechanisms of the 62 tRNA Codon Sequences
Fangping Wei1*, Zhenxiong Lan2, Luming Shen1, Bourong Liu1, Yu Xue1
Physical Science & Technology College, Guangxi University, Nanning, China
College of Computer and Information Engineering, Guangxi Teacther Education University, Nanning, China
1
2
How to cite this paper: Wei, F.P., Lan,
Z.X., Shen, L.M., Liu, B.R. and Xue, Y.
(2017) Comparison of Two Possible Evolutionary Mechanisms of the 62 tRNA Codon
Sequences. J. Biomedical Science and Engineering, 10, 172-181.
https://doi.org/10.4236/jbise.2017.104014
Received: March 1, 2017
Accepted: April 27, 2017
Published: April 30, 2017
Copyright © 2017 by authors and
Scientific Research Publishing Inc.
This work is licensed under the Creative
Commons Attribution International
License (CC BY 4.0).
http://creativecommons.org/licenses/by/4.0/
Open Access
Abstract
The tRNAs were divided into 62 groups based on the codons they carried and
networks were constructed. Phylogenetic trees were constructed in parallel
and antiparallel directions based on the parameters of these networks. Point
mutations were found in the codon sites in the same clusters in the entire parallel and antiparallel phylogenetic trees, whereas there was no evidence of a
complementary duplication mechanism in the corresponding antiparallel
phylogenetic trees. The codons of isoaccepting tRNAs were found in neighboring clusters or distributed within a very small distance so the codons with
only one base difference remained very close, which was perfectly consistent
with the hypothesis that a new tRNA gene could be recruited from an isoaccepting group via another point mutation.
Keywords
Phylogenetic Trees, Point Mutation, Template Duplication, Network
1. Introduction
There are many reports on mitochondrial (mt) tRNA mutations would linked
with inherited diseases [1] [2] [3], i.e., mutations in tRNAIle, tRNALys and tRNASer(UCN)
are known to cause different mt encephalomyopathies or non-syndromic
deafness [3]. The mutation of tRNA genes has a research hotspot. Many tRNA
sequences have been found and deposited in a database [4] and they all conform
to one of 62 codon sequence groups (two codon groups are absent from the database, i.e., aaa and cta). All modern tRNA sequences have evolved from a
common ancestor, but their evolutionary mechanism remains an open question.
Two possible mechanisms have been proposed to explain the origin and evolution of modern tRNAs, i.e., “point mutation” and “template duplication” [5].
The “point mutation” mechanism suggests that divergence occurred mainly via
DOI: 10.4236/jbise.2017.104014
April 30, 2017
F. P. Wei et al.
“mutation” [6] [7] [8] [9] [10]. It is hypothesized that a new sequence may be
recruited from the mutant RNA molecule or be recruited from an isoaccepting
group by another point mutation in the sequence that concurrently changed the
tRNA amino acid identity and its messenger RNA coupling capacity, which is
known as “codon capture” or “tRNA gene recruitment” [11]. In contrast to evolution via mutation, the “template duplication” mechanism proposes that tRNAs
diverged from a precursor via a duplication mechanism. It is hypothesized that
primordial tRNAs with hairpin structures associate themselves with a template
and produce another RNA via sequence complementarity [12]-[17]. It is thought
that four initial pairs of pre-tRNAs with complementary anti-codons could have
been capable of generating all 64 anticodons.
Theoretically, if modern tRNAs evolved via point mutations, the matching
scores of sequences that align in a parallel direction, 5’
3’ vs. 5’
should be larger than the scores aligned in an antiparallel direction, 5’
3’
3’,
3’ vs.
5’. If modern tRNAs evolve by complementary duplication method, how-
ever, the opposite would be true. To identify the most likely mechanism for
tRNA evolution, we compared tRNA sequences in parallel and antiparallel directions, and we constructed two types of networks to make a comparison. The
corresponding parallel and antiparallel phylogenetic trees of the 62 codon sequences could be generated by altering the parameters of these networks using
the neighbor-joining method to different degrees. We discuss the evolutionary
properties of the codon sequences for the 62 tRNA groups and the two types of
phylogenetic trees.
2. Materials and Methods
2.1. Experimental Data
The 3695 tRNA sequences are acquired from the database
(http://trnadb.bioinf.uni-leipzig.de/) [1] and the highly similar species in the database were filtered. Each tRNA sequence contained 76 bases and we removed
the bases in the variable stem and the poly-A tail.
2.2. tRNA Network Construction
2.2.1. Important Network Parameters
Degree and clustering coefficient: the network is made up of a set of nodes (vertices) and the connections between them (edges or links). The features and the
nature of the network were indicated by two main parameters [18], i.e., the degree, k, and the clustering coefficient, c, of the nodes. The degree k of a node was
the number of nodes with which it was connected. If a node connected with i
other nodes and j edges had connections within these i nodes, the clustering coefficient c of the original node was defined as
=
C 2 j i ( i − 1) , where i ( i − 1) 2
is the total number of possible connections among i nodes. The clustering coef-
ficient reflected the relationships among the neighbors of a node and it quantified the inherent tendency of the network to cluster. Investigating the degree and
clustering coefficient distribution of the network facilitated the study of the local
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F. P. Wei et al.
properties among the nodes and their global statistics.
2.2.2. Method for Constructing the tRNA Network
The steps used to construct the tRNA network were as follows.
(1) Compare the two tRNA sequences stochastically, ith and jth, in parallel
direction and antiparallel directions, and record their degree of similarity, sij
where sij is defined as the alignment scores for the ith and jth tRNAs (shown
in Figure 1)
(2) Consider each tRNA as one node in the network and add a connection if
two tRNAs have a degree of similarity, s, that is larger than a given degree of similarity s0 .
After repeating these two steps, an undirected tRNA network can be constructed based on a given degree of similarity. In this study, the 3695 tRNA sequences were divided into 62 groups based on their different tRNAs anticodons.
The networks were constructed using different degrees of similarity in parallel
and antiparallel directions, and the corresponding average degree
erage clustering coefficient
C
D
and av-
of these networks were recorded.
2.3. Phylogenetic Tree Construction
We constructed the tRNA phylogenetic trees suing the neighbor-joining method
[19]. To determine the evolutionary relationships among the 62 tRNA codon
sequences, we used a novel method to compute the evolutionary distances between different tRNAs groups using two important parameters, <D> and <C>,
for different networks of tRNAs, rather than comparing only two sequences. The
trees were constructed using the following steps.
(i) We used the ith and jth codon groups to produce larger tRNA groups and
used them to construct a network, before calculating the average degree
D ( i, j ) and the average clustering coefficient C ( i, j ) for this larger network.
(ii) The evolutionary distance between any two codon groups was computed
using the following equation:
1
 (1 − S L ) ∗ D ( i, j ) ( N − 1) + C ( i, j ) , i ≠ j
(1)
distance ( i, j ) =  2
0, i = j
(
)
Figure 1. The degree of similarity of two tRNA segments in two directions, parallel:
S = 8 , antiparallel: S = 15 . The alignment score was defined as the degree of similarity,
i.e., the number of bases in two tRNAs that were the same in a parallel comparison, such
as A-A, C-C, T-T, and G-G, or complementary in an antiparallel comparison, such as
A-T, C-G, and G-T.
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F. P. Wei et al.
where i and j ran from 1 to 62. In this study, L was the length of one tRNA, and
N was the total number of nodes in the network. We use D ( i, j ) and
C ( i, j ) to represent the alignment scores of two different codon groups,
which showed the evolutionary affiliation of tRNAs with two different codons,
which helped us to interpret the overall evolutionary trend of the tRNA sequences to some extent.
(iii) We constructed the phylogenetic tree for the 62 tRNA codon sequences
using PHYLIP 3.67 and TreeView 1.6.6.
3. Results
Figure 2 shows the diverse relationships among the phylogenetic trees of the 62
tRNA codon groups. Each tree branch represents one group with a specific codon sequence. Figure 2(a) shows that a degree of similarity of S = 10 produced two large clusters, i.e.,
((att,(cct,(act,(tgt,(tga,(cga,(tat,(tct,(gct,(aag:agt))))))))))),
(cgg,(tca,(gca,(agg,(tcg,(atc,(acc:acg))))))), gcc,(gcg,(gtg:tgg)) and
((cgc,(gta,(gtc,(gac,(aca,(ctg,(ggg:ccc)))))))),
agc,(cca,(acc,(gtt,(aga,(gga,(ctt:ggt)))))),ggc,(ctc,(tcc:ttg)), as well as 15 isolated
branches and one small cluster in the overall parallel phylogenetic tree, where
each large cluster comprised three small clusters. the sequences atg, aac, tta, ata,
caa, ttt, cat, gat, gag, tag, gaa, and taa were found in isolated branches, but their
evolutionary distance was small. They exhibited a regular ladder ranked appearance. All of the codons in the large clusters supported the point mutation mechanism and each had a matching codon with only one base difference in the
same site. We also found that some codons of the isoaccepting tRNAs appeared
in the same cluster and neighboring clusters. For example, six codons the amino
acid Arg, i.e., cct, tct, tcg, acg, ccg, and gcg, for were in the same cluster, three of
them were in a neighboring branch, and three were dispersed among different
branches. In contrast to the parallel phylogenetic tree for s = 10, the antiparallel
phylogenetic tree for s = 10 only contained two large clusters and some isolated
branches, and the codons of these two large clusters exhibited a regular laddered
rank. Thus, these results did not support “template duplication mechanism.”
Some codons of isoaccepting tRNA sequences also appeared in the same cluster,
e.g., four codons for Ser were in the same cluster, whereas the other two codons
were in another cluster. Most codons for isoaccepting tRNA sequences were
dispersed throughout the tree.
For s = 35, a comparison of Figure 2(a) and Figure 2(c) showed that the distribution of the parallel phylogenetic tree in Figure 2(c) was clearly different,
with fewer isolated branches while the codons in the large cluster were more
dispersed. Two small clusters and one large cluster comprised the whole tree,
where most codons had matching codons with only one base difference in the
small cluster, although a few had no mutated codons in the upstream branch.
More codons of the isoaccepting tRNA sequences were present in the same cluster and they were closer. As shown in Figure 2(d), the distribution of the anti175
F. P. Wei et al.
176
(a)
(b)
(c)
(d)
F. P. Wei et al.
(e)
(g)
(f)
(h)
Figure 2. Phylogenetic trees of 62 cod on sequences with a degree of similarity of s = 10, s = 35, s = 45 and s = 50 for the antiparallel phylogenetic tree and antiparallel phylogenetic tree. Each tree branch represents one group codon and its abbreviated letters.
The black solid dots () in the trees represent the codons that agree with the point mutation mechanism in a branch. (a) Parallel
phylogenetic tree with s = 10; (b) Antiparallel phylogenetic tree with s = 10; (c) Parallel phylogenetic tree with s = 35; (d) Antiparallel phylogenetic tree with s = 35; (e) Parallel phylogenetic tree with s = 45; (f) Antiparallel phylogenetic tree with s = 45; (g)
Parallel phylogenetic tree with s = 50; (h) Antiparallel phylogenetic tree with s = 50.
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parallel phylogenetic tree with s = 35 was more compact compared with the parallel phylogenetic tree with s = 35, i.e., three small clusters, one large cluster,
and two isolated branches comprised the entire tree. Two clusters formed the
core of the larger cluster. However, it appeared to be more disperse than the antiparallel phylogenetic tree with s = 10. Surprisingly, most of the codons in the
clusters did not have template duplication codons, even though they had copies
upstream. Their evolution did not agree with the “template duplication mechanism.”
As the degree of similarity (s) S increased, more dispersed clusters appeared in
the larger cluster in the parallel phylogenetic tree. As shown in Figure 2(e), the
largest cluster is divided into six small clusters with s = 45, where gtc, aac, tct,
and tcg remained in isolated branches. A comparison of Figure 2(a), Figure
2(c), and Figure 2(e) shows that the codon aac occupies a basal clade and it did
not vary with the degree of similarity (s) in the three phylogenetic trees. The
evolutionary relationships among the branches of the three phylogenetic trees
were always ordered and stable with different values of s. Most tRNA anticodons
in the same clusters had a high match with the “point mutation mechanism” and
most had only one base difference from the anticodon sites, which suggests that
they evolved by mutating from the same ancestral sequences via point mutations. At the same time, many isoaccepting tRNA codons were distributed in the
same cluster and they had a very compact structure. However, not all of the
isoaccepting tRNA codons had neighboring relationships, e.g., four codons in
the isoaccepting group for Arg were neighboring whereas the other two were far
from their branch, which suggested that these two codons may have evolved
from neighboring codons. In contrast to the sparse distribution of the parallel
phylogenetic tree, the antiparallel phylogenetic tree with s = 45 comprised two
large clusters with a more compact branch distribution. One large cluster also
appeared to have a laddered rank. Similar results are shown in Figure 2(f) where
more isoaccepting tRNA codons had neighbors in the same cluster, e.g., five codons for Leu were adjacent in a large cluster. However, not all of the isoaccepting tRNA codons were allocated to the same cluster. Figure 2(f) shows that evidence for duplication was absent from the entire tree.
As the degree of similarity s increased to 50, the distances of most codon
branches in the parallel and antiparallel phylogenetic trees tended toward 1, as
shown in Figure 2(g). The parallel phylogenetic trees with s = 50 displayed a
laddered rank, but there were few isolated branches and the distances among
most branches were similar. There were also many small clusters that contained
some codons of isoaccepting tRNAs. Most of these codons showed no evidence
point mutations traces at higher levels in the upstream branch. With s > 50, most
of the distances for the codons in the parallel phylogenetic trees were equal to 1.
There were clear differences in the parallel phylogenetic trees in Figure 2(h),
while most of the distances among codon branches in the antiparallel phylogenetic trees with s = 50 were equal to 1, and the distribution of the tree was a laddered rank.
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4. Conclusions
We constructed 62 × 61 2 groups of networks and eight phylogenetic trees of
tRNAs based on a point mutation mechanism and a complete duplication mechanism. We analyzed the features of each codon branch and the phylogenetic
trees in parallel and antiparallel directions. We found that point mutations had
an important role in the evolution of the 62 codon sequence groups. Point mutations were found in the codon sites in the same clusters in four complete parallel
phylogenetic trees, whereas there was no evidence for a complementary duplication mechanism in the corresponding antiparallel phylogenetic trees. In addition, many codons of isoaccepting tRNA were found in neighboring clusters or
very close clusters. The codons with one site difference were very close together.
These results support the hypothesis that new tRNA genes were recruited from
one isoacceptor group to another via a point mutation in the sequence.
Surprisingly, most of the codons in the antiparallel phylogenetic trees in the
same cluster did not have complementary copies without the point mutation
codons, although they were compared in the antiparallel direction. As shown in
Figure 3, most codons in the antiparallel phylogenetic tree with s = 45 had no
Figure 3. Codons in the antiparallel phylogenetic tree where s = 45 and its possible complementary duplication anticodons. The symbol “*” indicates that this anticodon has a
copy in the cluster.
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F. P. Wei et al.
complementary codons, although many had point mutation codons in the same
cluster. These observations also applied to the other antiparallel trees with different s values. They are marked with a black solid dot (●) in all of the trees and
they provide powerful support for the role of point mutations in the evolution of
the 64 tRNA codon sequences.
Point mutations occur in the mitochondria tRNA; some positions will cause
loss of stability or produce disease. As more and more tRNA sequencing, the
mutation of the tRNA gene sequences is studied further, and the evolutionary
mechanisms of the RNA will be proven.
Acknowledgements
This paper was supported by the National Science Foundation of Guanxi of China
(Grant No.: AE052095) and the National Regional Fund (Grant No.: 11262003)
and Guangxi Key Laboratory for the Relativistic Astrophysics.
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